Attachment 164517 Details for Bug 205525 – poudriere testport output for releng_9_3

poudriere testport output for releng_9_3

samtools-1.3_releng_9.txt (text/plain), 29.53 KB, created by cartwright on 2015-12-22 23:24:41 UTC

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Creator: cartwright

Created: 2015-12-22 23:24:41 UTC

Size: 29.53 KB

patch

obsolete

>[00:00:00] ====>> Creating the reference jail... done
>[00:00:00] ====>> Mounting system devices for releng_9_3-default
>[00:00:00] ====>> Mounting ports/packages/distfiles
>[00:00:00] ====>> Stashing existing package repository
>[00:00:00] ====>> Mounting packages from: /usr/local/poudriere/data/packages/releng_9_3-default
>[00:00:00] ====>> Copying /var/db/ports from: /usr/local/etc/poudriere.d/options
>[00:00:00] ====>> Appending to make.conf: /usr/local/etc/poudriere.d/make.conf
>/etc/resolv.conf -> /usr/local/poudriere/data/.m/releng_9_3-default/ref/etc/resolv.conf
>[00:00:00] ====>> Starting jail releng_9_3-default
>[00:00:00] ====>> Logs: /usr/local/poudriere/data/logs/bulk/releng_9_3-default/2015-12-22_16h07m13s
>[00:00:00] ====>> Loading MOVED
>[00:00:01] ====>> Calculating ports order and dependencies
>[00:00:02] ====>> Sanity checking the repository
>[00:00:02] ====>> Checking packages for incremental rebuild needed
>[00:00:03] ====>> Deleting htslib-1.2.1.txz: new version: 1.3
>[00:00:03] ====>> Deleting stale symlinks
>[00:00:03] ====>> Deleting empty directories
>[00:00:03] ====>> Cleaning the build queue
>[00:00:03] ====>> Recording filesystem state for prepkg... done
>[00:00:04] ====>> Building 1 packages using 1 builders
>[00:00:04] ====>> Starting/Cloning builders
>[00:00:05] ====>> Hit CTRL+t at any time to see build progress and stats
>[00:00:05] ====>> [01][00:00:00] Starting build of biology/htslib
>[00:00:56] ====>> [01][00:00:51] Finished build of biology/htslib: Success
>[00:00:57] ====>> Stopping 1 builders
>[00:01:00] ====>> Creating pkgng repository
>Creating repository in /tmp/packages: . done
>Packing files for repository: .... done
>[00:01:01] ====>> Committing packages to repository
>[00:01:01] ====>> Removing old packages
>[00:01:01] ====>> Portlint check
>WARN: /usr/local/poudriere/data/.m/releng_9_3-default/ref/usr/ports/biology/samtools/work/pkg-message: possible use of absolute pathname "/usr/local/bin/samto...".
>WARN: /usr/local/poudriere/data/.m/releng_9_3-default/ref/usr/ports/biology/samtools/work/pkg-message: possible direct use of "Add /usr/local" found. if so, use ${PREFIX} or ${LOCALBASE}, as appropriate.
>FATAL: work: be sure to cleanup the working directory before committing the port.
>1 fatal error and 2 warnings found.
>[00:01:02] ====>> Building with flags: 
>[00:01:02] ====>> Removing existing /usr/local
>build started at Tue Dec 22 16:08:15 MST 2015
>port directory: /usr/ports/biology/samtools
>building for: FreeBSD releng_9_3-default 9.3-RELEASE FreeBSD 9.3-RELEASE amd64
>maintained by: cartwright@asu.edu
>Makefile ident:      $FreeBSD: head/biology/samtools/Makefile 385521 2015-05-06 15:16:53Z mat $
>Poudriere version: 3.1.8
>Host OSVERSION: 1002000
>Jail OSVERSION: 903000
>
>---Begin Environment---
>PKGREPOSITORY=/tmp/pkgs
>PACKAGES=/tmp/pkgs
>OSVERSION=903000
>UNAME_v=FreeBSD 9.3-RELEASE
>UNAME_r=9.3-RELEASE
>BLOCKSIZE=K
>MAIL=/var/mail/root
>STATUS=1
>WARNING_WAIT=0
>SAVED_TERM=xterm-256color
>NO_WARNING_PKG_INSTALL_EOL=yes
>MASTERMNT=/usr/local/poudriere/data/.m/releng_9_3-default/ref
>FORCE_PACKAGE=yes
>PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin
>POUDRIERE_BUILD_TYPE=bulk
>OLDPWD=/usr/local/poudriere/data/.m/releng_9_3-default/ref/.p/pool
>PWD=/usr/local/poudriere/data/.m/releng_9_3-default/ref/usr/ports/biology/samtools
>MASTERNAME=releng_9_3-default
>SCRIPTPREFIX=/usr/local/share/poudriere
>USER=root
>HOME=/root
>POUDRIERE_VERSION=3.1.8
>SCRIPTPATH=/usr/local/share/poudriere/testport.sh
>TRYBROKEN=yes
>LIBEXECPREFIX=/usr/local/libexec/poudriere
>LOCALBASE=/usr/local
>PACKAGE_BUILDING=yes
>DEV_WARNING_WAIT=0
>---End Environment---
>
>---Begin OPTIONS List---
>---End OPTIONS List---
>
>--CONFIGURE_ARGS--
>--prefix=/usr/local ${_LATE_CONFIGURE_ARGS}
>--End CONFIGURE_ARGS--
>
>--CONFIGURE_ENV--
>MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl XDG_DATA_HOME=/wrkdirs/usr/ports/biology/samtools/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/samtools/work  HOME=/wrkdirs/usr/ports/biology/samtools/work TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=262144
>--End CONFIGURE_ENV--
>
>--MAKE_ENV--
>INSTALL_LIB="install  -s -m 444"  INSTALL_DATA="install  -m 0644"  INSTALL_PROGRAM="install  -s -m 555"  INSTALL_SCRIPT="install  -m 555"  INSTALL_DIR="/bin/mkdir -p" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/samtools/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/samtools/work  HOME=/wrkdirs/usr/ports/biology/samtools/work TMPDIR="/tmp" NO_PIE=yes NO_DEBUG_FILES=yes SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local  LOCALBASE=/usr/local  LIBDIR="/usr/lib"  CC="cc" CFLAGS="-O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector"  CPP="cpp" CPPFLAGS="-I/usr/local/include"  LDFLAGS=" -L/usr/local/lib -fstack-protector" LIBS=""  CXX="c++" CXXFLAGS="-O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector"  MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install  -s -m 555"  BSD_INSTALL_LIB="install  -s -m 444"  BSD_INSTALL_SCRIPT="install  -m 555"  BSD_INSTALL_DATA="install  -m 0644"  BSD_INSTALL_MAN="install  -m 444"
>--End MAKE_ENV--
>
>--PLIST_SUB--
>PORTVERSION="1.3"
>OSREL=9.3
>PREFIX=%D
>LOCALBASE=/usr/local
>RESETPREFIX=/usr/local
>PORTDOCS=""
>PORTEXAMPLES=""
>LIB32DIR=lib
>PERL_VERSION=5.20.3
>PERL_VER=5.20
>PERL5_MAN1=lib/perl5/site_perl/man/man1
>PERL5_MAN3=lib/perl5/site_perl/man/man3
>SITE_PERL=lib/perl5/site_perl
>SITE_ARCH=lib/perl5/site_perl/mach/5.20
>DOCSDIR="share/doc/samtools"
>EXAMPLESDIR="share/examples/samtools"
>DATADIR="share/samtools"
>WWWDIR="www/samtools"
>ETCDIR="etc/samtools"
>--End PLIST_SUB--
>
>--SUB_LIST--
>PREFIX=/usr/local
>LOCALBASE=/usr/local
>DATADIR=/usr/local/share/samtools
>DOCSDIR=/usr/local/share/doc/samtools
>EXAMPLESDIR=/usr/local/share/examples/samtools
>WWWDIR=/usr/local/www/samtools
>ETCDIR=/usr/local/etc/samtools
>--End SUB_LIST--
>
>---Begin make.conf---
>USE_PACKAGE_DEPENDS=yes
>BATCH=yes
>WRKDIRPREFIX=/wrkdirs
>USE_PACKAGE_DEPENDS=yes
>BATCH=yes
>WRKDIRPREFIX=/wrkdirs
>PORTSDIR=/usr/ports
>PACKAGES=/packages
>DISTDIR=/distfiles
>#### /usr/local/etc/poudriere.d/make.conf ####
>CFLAGS += -O2 -fno-strict-aliasing -pipe
>
>#DEFAULT_VERSIONS=python=2.7 python2=2.7 python3=3.4
>#WITH_BDB_VER=6
>#WITH_BDB6_PERMITTED=yes
>TEX_DEFAULT=texlive
>
>MAKE_JOBS_NUMBER_LIMIT=8
>
>---End make.conf---
>=======================<phase: check-sanity   >============================
>===>  License MIT accepted by the user
>===========================================================================
>=======================<phase: pkg-depends    >============================
>===>   samtools-1.3 depends on file: /usr/local/sbin/pkg - not found
>===>   Installing existing package /packages/All/pkg-1.6.2.txz
>[releng_9_3-default] Installing pkg-1.6.2...
>[releng_9_3-default] Extracting pkg-1.6.2: .......... done
>Message from pkg-1.6.2:
>If you are upgrading from the old package format, first run:
>
>  # pkg2ng
>===>   samtools-1.3 depends on file: /usr/local/sbin/pkg - found
>===>   Returning to build of samtools-1.3
>===========================================================================
>=======================<phase: fetch-depends  >============================
>===========================================================================
>=======================<phase: fetch          >============================
>===>  License MIT accepted by the user
>===>   samtools-1.3 depends on file: /usr/local/sbin/pkg - found
>===> Fetching all distfiles required by samtools-1.3 for building
>===========================================================================
>=======================<phase: checksum       >============================
>===>  License MIT accepted by the user
>===>   samtools-1.3 depends on file: /usr/local/sbin/pkg - found
>===> Fetching all distfiles required by samtools-1.3 for building
>=> SHA256 Checksum OK for samtools-samtools-1.3_GH0.tar.gz.
>===========================================================================
>=======================<phase: extract-depends>============================
>===========================================================================
>=======================<phase: extract        >============================
>===>  License MIT accepted by the user
>===>   samtools-1.3 depends on file: /usr/local/sbin/pkg - found
>===> Fetching all distfiles required by samtools-1.3 for building
>===>  Extracting for samtools-1.3
>=> SHA256 Checksum OK for samtools-samtools-1.3_GH0.tar.gz.
>===========================================================================
>=======================<phase: patch-depends  >============================
>===========================================================================
>=======================<phase: patch          >============================
>===>  Patching for samtools-1.3
>===>  Applying FreeBSD patches for samtools-1.3
>/bin/cp /usr/ports/biology/samtools/files/ax_with_htslib.m4 /wrkdirs/usr/ports/biology/samtools/work/samtools-1.3/
>/bin/cp /usr/ports/biology/samtools/files/ax_with_curses.m4 /wrkdirs/usr/ports/biology/samtools/work/samtools-1.3/
>===========================================================================
>=======================<phase: build-depends  >============================
>===>   samtools-1.3 depends on package: htslib>=1.3 - not found
>===>   Installing existing package /packages/All/htslib-1.3.txz
>[releng_9_3-default] Installing htslib-1.3...
>[releng_9_3-default] `-- Installing curl-7.46.0_1...
>[releng_9_3-default] |   `-- Installing ca_root_nss-3.20.1...
>[releng_9_3-default] |   `-- Extracting ca_root_nss-3.20.1: ....... done
>[releng_9_3-default] `-- Extracting curl-7.46.0_1: .......... done
>[releng_9_3-default] Extracting htslib-1.3: .......... done
>Message from ca_root_nss-3.20.1:
>********************************* WARNING *********************************
>
>FreeBSD does not, and can not warrant that the certification authorities
>whose certificates are included in this package have in any way been
>audited for trustworthiness or RFC 3647 compliance.
>
>Assessment and verification of trust is the complete responsibility of the
>system administrator.
>
>*********************************** NOTE **********************************
>
>This package installs symlinks to support root certificates discovery by
>default for software that uses OpenSSL.
>
>This enables SSL Certificate Verification by client software without manual
>intervention.
>
>If you prefer to do this manually, replace the following symlinks with
>either an empty file or your site-local certificate bundle.
>
>  * /etc/ssl/cert.pem
>  * /usr/local/etc/ssl/cert.pem
>  * /usr/local/openssl/cert.pem
>
>***************************************************************************
>===>   samtools-1.3 depends on package: htslib>=1.3 - found
>===>   Returning to build of samtools-1.3
>===>   samtools-1.3 depends on executable: autoconf-2.69 - not found
>===>   Installing existing package /packages/All/autoconf-2.69.txz
>[releng_9_3-default] Installing autoconf-2.69...
>[releng_9_3-default] `-- Installing indexinfo-0.2.4...
>[releng_9_3-default] `-- Extracting indexinfo-0.2.4: .... done
>[releng_9_3-default] `-- Installing autoconf-wrapper-20131203...
>[releng_9_3-default] `-- Extracting autoconf-wrapper-20131203: ........ done
>[releng_9_3-default] `-- Installing perl5-5.20.3_8...
>[releng_9_3-default] `-- Extracting perl5-5.20.3_8: .......... done
>[releng_9_3-default] `-- Installing m4-1.4.17_1,1...
>[releng_9_3-default] `-- Extracting m4-1.4.17_1,1: .......... done
>[releng_9_3-default] Extracting autoconf-2.69: .......... done
>Message from perl5-5.20.3_8:
>The /usr/bin/perl symlink has been removed starting with Perl 5.20.
>For shebangs, you should either use:
>
>#!/usr/local/bin/perl
>
>or
>
>#!/usr/bin/env perl
>
>The first one will only work if you have a /usr/local/bin/perl,
>the second will work as long as perl is in PATH.
>===>   samtools-1.3 depends on executable: autoconf-2.69 - found
>===>   Returning to build of samtools-1.3
>===>   samtools-1.3 depends on executable: autoheader-2.69 - found
>===>   samtools-1.3 depends on executable: autoreconf-2.69 - found
>===>   samtools-1.3 depends on executable: aclocal-1.15 - not found
>===>   Installing existing package /packages/All/automake-1.15_1.txz
>[releng_9_3-default] Installing automake-1.15_1...
>[releng_9_3-default] `-- Installing automake-wrapper-20131203...
>[releng_9_3-default] `-- Extracting automake-wrapper-20131203: ... done
>[releng_9_3-default] Extracting automake-1.15_1: .......... done
>===>   samtools-1.3 depends on executable: aclocal-1.15 - found
>===>   Returning to build of samtools-1.3
>===>   samtools-1.3 depends on executable: automake-1.15 - found
>===>   samtools-1.3 depends on executable: gmake - not found
>===>   Installing existing package /packages/All/gmake-4.1_2.txz
>[releng_9_3-default] Installing gmake-4.1_2...
>[releng_9_3-default] `-- Installing libiconv-1.14_9...
>[releng_9_3-default] `-- Extracting libiconv-1.14_9: .......... done
>[releng_9_3-default] `-- Installing gettext-runtime-0.19.6...
>[releng_9_3-default] `-- Extracting gettext-runtime-0.19.6: .......... done
>[releng_9_3-default] Extracting gmake-4.1_2: .......... done
>===>   samtools-1.3 depends on executable: gmake - found
>===>   Returning to build of samtools-1.3
>===========================================================================
>=======================<phase: lib-depends    >============================
>===>   samtools-1.3 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so)
>===========================================================================
>====>> Recording filesystem state for prebuild... done
>=======================<phase: configure      >============================
>===>   samtools-1.3 depends on package: htslib>=1.3 - found
>===>   samtools-1.3 depends on executable: autoconf-2.69 - found
>===>   samtools-1.3 depends on executable: autoheader-2.69 - found
>===>   samtools-1.3 depends on executable: autoreconf-2.69 - found
>===>   samtools-1.3 depends on executable: aclocal-1.15 - found
>===>   samtools-1.3 depends on executable: automake-1.15 - found
>===>   samtools-1.3 depends on executable: gmake - found
>===>   samtools-1.3 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so)
>===>  Configuring for samtools-1.3
>configure: loading site script /usr/ports/Templates/config.site
>checking for gcc... cc
>checking whether the C compiler works... yes
>checking for C compiler default output file name... a.out
>checking for suffix of executables... 
>checking whether we are cross compiling... no
>checking for suffix of object files... o
>checking whether we are using the GNU C compiler... yes
>checking whether cc accepts -g... yes
>checking for cc option to accept ISO C89... none needed
>checking location of HTSlib source tree... none found
>checking for htslib/sam.h... yes
>checking for hts_version in -lhts... yes
>checking for NcursesW wide-character library... yes
>checking for working ncursesw/curses.h... no
>checking for working ncursesw.h... no
>checking for working ncurses.h... yes
>checking for zlib.h... (cached) yes
>checking for inflate in -lz... yes
>configure: creating ./config.status
>config.status: creating config.mk
>config.status: creating config.h
>===========================================================================
>=======================<phase: build          >============================
>===>  Building for samtools-1.3
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o bam_index.o bam_index.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o bam_plcmd.o bam_plcmd.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o sam_view.o sam_view.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o bam_cat.o bam_cat.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o bam_md.o bam_md.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o bam_reheader.o bam_reheader.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o bam_sort.o bam_sort.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o bedidx.o bedidx.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o kprobaln.o kprobaln.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o bam_rmdup.o bam_rmdup.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o bam_rmdupse.o bam_rmdupse.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o bam_mate.o bam_mate.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o bam_stat.o bam_stat.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o bam_color.o bam_color.c
>echo '#define SAMTOOLS_VERSION "1.3"' > version.h
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o bam2bcf.o bam2bcf.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o bam2bcf_indel.o bam2bcf_indel.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o errmod.o errmod.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o sample.o sample.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o sam_opts.o sam_opts.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o cut_target.o cut_target.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o phase.o phase.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o bam2depth.o bam2depth.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o padding.o padding.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o bedcov.o bedcov.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o bamshuf.o bamshuf.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o faidx.o faidx.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o dict.o dict.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o stats.o stats.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o stats_isize.o stats_isize.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o bam_flags.o bam_flags.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o bam_split.o bam_split.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o bam_tview.o bam_tview.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o bam_tview_curses.o bam_tview_curses.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o bam_tview_html.o bam_tview_html.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o bam_lpileup.o bam_lpileup.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o bam_quickcheck.o bam_quickcheck.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o bam_addrprg.o bam_addrprg.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o bam_aux.o bam_aux.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o bam.o bam.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o bam_import.o bam_import.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o sam.o sam.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o sam_header.o sam_header.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o bam_plbuf.o bam_plbuf.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o misc/ace2sam.o misc/ace2sam.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -DMAQ_LONGREADS -I.  -I/usr/local/include -c -o misc/maq2sam-long.o misc/maq2sam.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o misc/maq2sam-short.o misc/maq2sam.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o misc/md5fa.o misc/md5fa.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o misc/md5sum-lite.o misc/md5sum-lite.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o misc/wgsim.o misc/wgsim.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o test/test.o test/test.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o test/split/test_count_rg.o test/split/test_count_rg.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o test/split/test_parse_args.o test/split/test_parse_args.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o test/vcf-miniview.o test/vcf-miniview.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o bamtk.o bamtk.c
>ar -csru libbam.a bam_aux.o bam.o bam_import.o sam.o sam_header.o bam_plbuf.o
>cc -L/usr/local/lib -fstack-protector -o misc/maq2sam-long misc/maq2sam-long.o -lz 
>cc -L/usr/local/lib -fstack-protector -o misc/maq2sam-short misc/maq2sam-short.o -lz 
>cc -rdynamic  -L/usr/local/lib -fstack-protector -o misc/md5fa misc/md5fa.o -lhts -lz 
>cc -rdynamic  -L/usr/local/lib -fstack-protector -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz 
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I.  -I/usr/local/include -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
>cc -pthread -rdynamic  -L/usr/local/lib -fstack-protector -o test/vcf-miniview test/vcf-miniview.o -lhts -lz 
>cc -pthread -rdynamic  -L/usr/local/lib -fstack-protector -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o sam_opts.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o libbam.a -lhts -lncursesw -lm -lz 
>cc -L/usr/local/lib -fstack-protector -o misc/ace2sam misc/ace2sam.o -lz 
>cc -L/usr/local/lib -fstack-protector -o misc/wgsim misc/wgsim.o -lm -lz 
>cc -pthread -rdynamic  -L/usr/local/lib -fstack-protector -o test/split/test_count_rg test/split/test_count_rg.o test/test.o sam_opts.o -lhts -lz 
>cc -pthread -rdynamic  -L/usr/local/lib -fstack-protector -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o sam_opts.o -lhts -lz 
>cc -pthread -rdynamic  -L/usr/local/lib -fstack-protector -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o sam_opts.o -lhts -lz 
>cc -pthread -rdynamic  -L/usr/local/lib -fstack-protector -o test/split/test_parse_args test/split/test_parse_args.o test/test.o sam_opts.o -lhts -lz 
>cc -pthread -rdynamic  -L/usr/local/lib -fstack-protector -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o sam_opts.o -lhts -lz 
>cc -pthread -rdynamic  -L/usr/local/lib -fstack-protector -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o sam_opts.o -lhts -lz 
>cc -pthread -rdynamic  -L/usr/local/lib -fstack-protector -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o sam_opts.o -lhts -lz 
>===========================================================================
>====>> Checking for filesystem violations... done
>=======================<phase: run-depends    >============================
>===========================================================================
>====>> Recording filesystem state for prestage... done
>=======================<phase: stage          >============================
>===>  Staging for samtools-1.3
>===>   samtools-1.3 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so)
>===>   Generating temporary packing list
>/bin/mkdir -p /wrkdirs/usr/ports/biology/samtools/work/stage/usr/local/bin /wrkdirs/usr/ports/biology/samtools/work/stage/usr/local/bin/samtools_misc /wrkdirs/usr/ports/biology/samtools/work/stage/usr/local/man/man1 
>install  -s -m 555 samtools /wrkdirs/usr/ports/biology/samtools/work/stage/usr/local/bin
>install  -s -m 555 misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim /wrkdirs/usr/ports/biology/samtools/work/stage/usr/local/bin/samtools_misc
>install  -m 555 misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/varfilter.py misc/wgsim_eval.pl misc/zoom2sam.pl /wrkdirs/usr/ports/biology/samtools/work/stage/usr/local/bin/samtools_misc
>install  -m 0644 samtools.1 misc/wgsim.1 /wrkdirs/usr/ports/biology/samtools/work/stage/usr/local/man/man1
>====> Compressing man pages (compress-man)
>===========================================================================
>====> Running Q/A tests (stage-qa)
>====> Checking for pkg-plist issues (check-plist)
>===> Parsing plist
>===> Checking for items in STAGEDIR missing from pkg-plist
>===> Checking for items in pkg-plist which are not in STAGEDIR
>===> No pkg-plist issues found (check-plist)
>====>> Checking for staging violations... done
>=======================<phase: package        >============================
>===>  Building package for samtools-1.3
>===========================================================================
>=======================<phase: install-mtree  >============================
>===========================================================================
>====>> Recording filesystem state for preinst... done
>=======================<phase: install        >============================
>===>  Installing for samtools-1.3
>===>   samtools-1.3 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so)
>===>  Checking if samtools already installed
>===>   Registering installation for samtools-1.3
>[releng_9_3-default] Installing samtools-1.3...
>The miscellaneous tools included with Samtools have been installed to /usr/local/bin/samtools_misc. Add that directory to your path if you want to use these tools.
>
>Some of these tools depend on Perl5, and it will need to be installed to use them.
>
>===========================================================================
>====>> Checking shared library dependencies
> 0x0000000000000001 (NEEDED)             Shared library: [libc.so.7]
> 0x0000000000000001 (NEEDED)             Shared library: [libhts.so.1]
> 0x0000000000000001 (NEEDED)             Shared library: [libm.so.5]
> 0x0000000000000001 (NEEDED)             Shared library: [libncursesw.so.8]
> 0x0000000000000001 (NEEDED)             Shared library: [libthr.so.3]
> 0x0000000000000001 (NEEDED)             Shared library: [libz.so.6]
>=======================<phase: deinstall      >============================
>===>  Deinstalling for samtools
>===>   Deinstalling samtools-1.3
>Updating database digests format: .......... done
>Checking integrity... done (0 conflicting)
>Deinstallation has been requested for the following 1 packages (of 0 packages in the universe):
>
>Installed packages to be REMOVED:
>	samtools-1.3
>
>The operation will free 640 KiB.
>[releng_9_3-default] [1/1] Deinstalling samtools-1.3...
>[releng_9_3-default] [1/1] Deleting files for samtools-1.3: .......... done
>===========================================================================
>====>> Checking for extra files and directories
>[00:01:21] ====>> Installing from package
>[releng_9_3-default] Installing samtools-1.3...
>[releng_9_3-default] Extracting samtools-1.3: .......... done
>Message from samtools-1.3:
>The miscellaneous tools included with Samtools have been installed to /usr/local/bin/samtools_misc. Add that directory to your path if you want to use these tools.
>
>Some of these tools depend on Perl5, and it will need to be installed to use them.
>[00:01:21] ====>> Cleaning up
>===>  Cleaning for samtools-1.3
>[00:01:21] ====>> Deinstalling package
>Updating database digests format: . done
>Checking integrity... done (0 conflicting)
>Deinstallation has been requested for the following 1 packages (of 0 packages in the universe):
>
>Installed packages to be REMOVED:
>	samtools-1.3
>
>The operation will free 640 KiB.
>[releng_9_3-default] [1/1] Deinstalling samtools-1.3...
>[releng_9_3-default] [1/1] Deleting files for samtools-1.3: .......... done
>build of biology/samtools ended at Tue Dec 22 16:08:34 MST 2015
>build time: 00:00:19
>[00:01:22] ====>> Cleaning up
>[00:01:22] ====>> Umounting file systems

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Attachments on bug 205525: 164514 | 164515 | 164517